Cooperative binding of aflatoxin B1 by cytochrome P450 3A4: a computational study

Metabolic transformation of cyclopiazonic acid in liver microsomes from different species based on UPLC-Q/TOF-MS

To investigate the metabolic transformation of cyclopiazonic acid (CPA) in the liver of different species and to supplement accurate risk assessment information, the metabolism of CPA in liver microsomes from four animals and humans was studied using the ultra-high-performance liquid chromatography-quadrupole/time-of-flight method. The results showed that a total of four metabolites were obtained, and dehydrogenation, hydroxylation, methylation, and glucuronidation were identified as the main metabolic pathways of CPA. Rat liver microsomes exhibited the highest metabolic capacity for CPA, with dehydrogenated (C20H18N2O3) and glucuronic acid-conjugated (C26H28N2O10) metabolites identified in all liver microsomes except chicken, indicating significant species metabolic differences. Moreover, C20H18N2O3 was only detected in the incubation system with cytochromes P450 3A4 (CYP3A4). The hydroxylated (C20H20N2O4) and methylated (C21H22N2O3) metabolites were detected in all incubation systems except for the CYP2C9, with CYP3A4 demonstrating the strongest metabolic capacity. The "cocktail" probe drug method showed that CPA exhibited a moderate inhibitory effect on the CYP3A4 (IC50 value = 8.658 μM), indicating that the substrate had a negative effect on enzyme activity. Our results provide new insights to understand the biotransformation profile of CPA in animals and humans.

Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes

Cytochrome P450 3A4 (CYP3A4) is one of the most important drug-metabolizing enzymes in the human body and is well known for its complicated, atypical kinetic characteristics. The existence of multiple ligand-binding sites in CYP3A4 has been widely recognized as being capable of interfering with the active pocket through allosteric effects. The identification of ligand-binding sites other than the canonical active site above the heme is especially important for understanding the atypical kinetic characteristics of CYP3A4 and the intriguing association between the ligand and the receptor. In this study, we first employed mixed-solvent molecular dynamics (MixMD) simulations coupled with the online computational predictive tools to explore potential ligand-binding sites in CYP3A4. The MixMD approach demonstrates better performance in dealing with the receptor flexibility compared with other computational tools. From the sites identified by MixMD, we then picked out multiple sites for further exploration using ensemble docking and conventional molecular dynamics (cMD) simulations. Our results indicate that three extra sites are suitable for ligand binding in CYP3A4, including one experimentally confirmed site and two novel sites.

Mycoviruses in Fungi: Carcinogenesis of Fungal Agents May Not Always Be Mycotoxin Related

Certain viruses have been found to induce diverse biological pathways to carcinogenesis, evidenced by the presence of viral gene products in some tumors. Despite the fact that many fungal agents contain mycoviruses, until recently, their possible direct effects on human health, including carcinogenesis and leukemogenesis, had not been explored. In this regard, most studies of fungal agents have rightly concentrated on their mycotoxin formation and effects. Recently, the direct role of yeasts and fungi in the etiology of cancers, including leukemia, have been investigated. While greater attention has been placed on the carcinogenic effects of Candida, the role of filamentous fungi in carcinogenesis has also been explored. Recent findings from studies using the enzyme-linked immunosorbent assay (ELISA) technique indicate that the plasma of patients with acute lymphoblastic leukemia (ALL) uniformly contains antibodies for a certain mycovirus-containing Aspergillus flavus, while controls are negative. The exposure of mononuclear leukocytes from patients with ALL in full remission, and long-term survivors, to the product of this organism was reported to result in the re-development of typical genetics and cell surface phenotypes characteristic of active ALL. Mycoviruses are known to be able to significantly alter the biological characteristics and functions of their host. The possible carcinogenic and leukemogenic role of mycoviruses, with and without their host, needs to be further investigated.

Computational Studies of Aflatoxin B1 (AFB1): A Review

Aflatoxin B₁ (AFB₁) exhibits the most potent mutagenic and carcinogenic activity among aflatoxins. For this reason, AFB₁ is recognized as a human group 1 carcinogen by the International Agency of Research on Cancer. Consequently, it is essential to determine its properties and behavior in different chemical systems. The chemical properties of AFB₁ can be explored using computational chemistry, which has been employed complementarily to experimental investigations. The present review includes in silico studies (semiempirical, Hartree-Fock, DFT, molecular docking, and molecular dynamics) conducted from the first computational study in 1974 to the present (2022). This work was performed, considering the following groups: (a) molecular properties of AFB₁ (structural, energy, solvent effects, ground and the excited state, atomic charges, among others); (b) theoretical investigations of AFB₁ (degradation, quantification, reactivity, among others); (c) molecular interactions with inorganic compounds (Ag⁺, Zn²⁺, and Mg²⁺); (d) molecular interactions with environmentally compounds (clays); and (e) molecular interactions with biological compounds (DNA, enzymes, cyclodextrins, glucans, among others). Accordingly, in this work, we provide to the stakeholder the knowledge of toxicity of types of AFB₁-derivatives, the structure-activity relationships manifested by the bonds between AFB₁ and DNA or proteins, and the types of strategies that have been employed to quantify, detect, and eliminate the AFB₁ molecule.

Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin

CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production of the cholesterol-lowering drug pravastatin, the stereoselectivity of the enzyme needs to be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In the current study, we report further optimization of the stereoselectivity by a computationally aided approach. Using the CoupledMoves protocol of Rosetta, a virtual library of mutants was designed to bind compactin in a pro-pravastatin orientation. By examining the frequency of occurrence of beneficial substitutions and rational inspection of their interactions, a small set of eight mutants was predicted to show the desired selectivity and these variants were tested experimentally. The best CYP105AS1 variant gave >99% stereoselective hydroxylation of compactin to pravastatin, with complete elimination of the unwanted 6-epi-pravastatin diastereomer. The enzyme-substrate complexes were also examined by ultrashort molecular dynamics simulations of 50 × 100 ps and 5 × 22 ns, which revealed that the frequency of occurrence of near-attack conformations agreed with the experimentally observed stereoselectivity. These results show that a combination of computational methods and rational inspection could improve CYP105AS1 stereoselectivity beyond what was obtained by directed evolution. Moreover, the work lays out a general in silico framework for specificity engineering of enzymes of known structure.

Enhancing the detection sensitivity of nanobody against aflatoxin B1 through structure-guided modification

Nanobodies (Nbs) have shown great potential in immunodetection of small-molecule contaminants in food and environmental monitoring. However, the limited knowledge of the mechanism of Nbs binding to small molecules has hampered the development of high-affinity Nbs and assay improvement. We previously reported two homologous nanobodies Nb26 and Nb28 specific to aflatoxin B₁ (AFB₁), with the former exhibiting higher sensitivity in ELISA. Herein, Nb26 was selected as the model antibody to resolve its solution nuclear magnetic resonance (NMR) structure, and investigate its AFB₁ recognition mechanism. The results revealed that Nb26 exhibits a typical immunoglobulin fold and its AFB₁-binding interface is uniquely located in complementarity-determining region 3 (CDR3) and framework region 2 (FR2). This finding was applied to improve the binding activity of Nb28 against AFB₁ by constructing two Nb28-based mutants A⁵⁰V and S¹⁰²D, resulting in 2.3- and 3.3-fold sensitivity enhancement over the wild type, respectively. This study develops an NMR-based strategy to analyze the underlying mechanism of Nb against AFB₁, and successfully generated two site-modified Nbs with improved detection sensitivity. It is believed that this work could greatly expand the applications of Nbs by providing a way to enhance the binding activity.

Mango (Mangifera indica L.) Polyphenols: Anti-Inflammatory Intestinal Microbial Health Benefits, and Associated Mechanisms of Actions

Mango is rich in polyphenols including gallotannins and gallic acid, among others. The bioavailability of mango polyphenols, especially polymeric gallotannins, is largely dependent on the intestinal microbiota, where the generation of absorbable metabolites depends on microbial enzymes. Mango polyphenols can favorably modulate bacteria associated with the production of bioactive gallotannin metabolites including Lactobacillus plantarum, resulting in intestinal health benefits. In several studies, the prebiotic effects of mango polyphenols and dietary fiber, their potential contribution to lower intestinal inflammation and promotion of intestinal integrity have been demonstrated. Additionally, polyphenols occurring in mango have some potential to interact with intestinal and less likely with hepatic enzymes or transporter systems. This review provides an overview of interactions of mango polyphenols with the intestinal microbiome, associated health benefits and underlying mechanisms.

Renal Transcriptomics Reveals the Carcinogenic Mechanism of Ethyl Carbamate in Musalais

INTRODUCTION

Musalais is a traditional fermented wine produced in southern Xinjiang (a province of China) and is protected as a form of national intangible cultural heritage. However, ethyl carbamate (EC), which is naturally produced during the fermentation process, has been shown to induce carcinogenesis and was classified as a group 2A carcinogen by The World Health Organization's International Agency for Research on Cancer.

METHODS

In this work, rats were treated with musalais containing EC at varying contents (0.1, 1, or 10 mg/kg). To evaluate the toxicity of EC in musalais, the liver and kidney of the rats were subjected to transcriptomics sequencing. Differentially expressed genes (DEGs) between treated and untreated rats were identified, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed on these genes to investigate the biological functions affected by EC in musalais.

RESULTS

The results demonstrated that high EC content in musalais is possibly involved in the regulation of cytochrome P450 metabolism, chemical carcinogenesis, metabolism of xenobiotics by cytochrome P450, Wnt signaling, and p53 signaling by targeting Mgst1, Gstp1, Gsta5, Gsta1, Adh1, Gsta2, and Ccnd1, thereby inducing cancer.

CONCLUSION

The present work predicted the potential carcinogenic mechanism of high EC content in musalais, providing a reference for its safety evaluation.

Discovery of potential targets of Triptolide through inverse docking in ovarian cancer cells

Triptolide (TPL) is proposed as an effective anticancer agent known for its anti-proliferation of a variety of cancer cells including ovarian cancer cells. Although some studies have been conducted, the mechanism by which TPL acts on ovarian cancer remains to be clearly described. Herein, systematic work based on bioinformatics was carried out to discover the potential targets of TPL in SKOV-3 cells. TPL induces the early apoptosis of SKOV-3 cells in a dose- and time-dependent manner with an IC₅₀ = 40 ± 0.89 nM when cells are incubated for 48 h. Moreover, 20 nM TPL significantly promotes early apoptosis at a rate of 40.73%. Using a self-designed inverse molecular docking protocol, we fish the top 19 probable targets of TPL from the target library, which was built on 2,250 proteins extracted from the Protein Data Bank. The 2D-DIGE assay reveals that the expression of eight genes is affected by TPL. The results of western blotting and qRT-PCR assay suggest that 40 nM of TPL up-regulates the level of Annexin A5 (6.34 ± 0.07 fold) and ATP syn thase (4.08 ± 0.08 fold) and down-regulates the level of β-Tubulin (0.11 ± 0.12 fold) and HSP90 (0.21 ± 0.09 fold). More details of TPL affecting on Annexin A5 signaling pathway will be discovered in the future. Our results define some potential targets of TPL, with the hope that this agent could be used as therapy for the preclinical treatment of ovarian cancer.

The Multifarious Link between Cytochrome P450s and Cancer

Cancer is a leading cause of death worldwide. Cytochrome P450s (P450s) play an important role in the metabolism of endogenous as well as exogenous substances, especially drugs. Moreover, many P450s can serve as targets for disease therapy. Increasing reports of epidemiological, diagnostic, and clinical research indicate that P450s are enzymes that play a major part in the formation of cancer, prevention, and metastasis. The purposes of this review are to shed light on the current state of knowledge about the cancer molecular mechanism involving P450s and to summarize the link between the cancer effects and the participation of P450s.

Analysis of the Molecular Interactions between Cytochromes P450 3A4 and 1A2 and Aflatoxins: A Docking Study

Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 were analyzed using density functional theory. Different methodologies—B3LYP/6-311G(d,p) and M06-2X/6-311G(d,p)—were applied for geometrical calculations. Chemical reactivity parameters were used in the calculation of charge transfer values during the interaction between protein and ligand. The binding energy, the electrostatic interactions, and the amino acids of the active site were determined by molecular docking analysis between AF and cytochromes P450 (3A4 and 1A2), employing different PDB files (CYP3A4:1TQN, 2V0M, 4NY4 and 1W0E, and CYP1A2:2HI4). Molecular docking analysis indicated that the central rings of the AF are involved in the interaction with the HEM group of the active site. The differences in the molecular structure of the AF affect their position regarding the HEM group. The resulting configurations presented considerable variation in the amino acids and the position of the coupling. The charge transfer values showed that there is oxidative damage inside the active site and that the HEM group is responsible for the main charge transferences.

Binding Modes and Metabolism of Caffeine

A correct estimate of ligand binding modes and a ratio of their occupancies is crucial for calculations of binding free energies. The newly developed method BLUES combines molecular dynamics with nonequilibrium candidate Monte Carlo. Nonequilibrium candidate Monte Carlo generates a plethora of possible binding modes and molecular dynamics enables the system to relax. We used BLUES to investigate binding modes of caffeine in the active site of its metabolizing enzyme Cytochrome P450 1A2 with the aim of elucidating metabolite-formation profiles at different concentrations. Because the activation energies of all sites of metabolism do not show a clear preference for one metabolite over the others, the orientations in the active site must play a key role. In simulations with caffeine located in a spacious pocket above the I-helix, it points N3 and N1 to the heme iron, whereas in simulations where caffeine is in close proximity to the heme N7 and C8 are preferably oriented toward the heme iron. We propose a mechanism where at low caffeine concentrations caffeine binds to the upper part of the active site, leading to formation of the main metabolite paraxanthine. On the other hand, at high concentrations two molecules are located in the active site, forcing one molecule into close proximity to the heme and yielding metabolites theophylline and trimethyluretic acid. Our results offer an explanation of previously published experimental results.

A theoretical insight into the reaction mechanisms of a 2,4,6-trinitrotoluene nitroso metabolite with thiols for toxic effects

2,4,6-Trinitrotoluene (TNT) is a class C carcinogen as rated by the Environmental Protection Agency. One of the toxicity mechanisms of TNT is the covalent binding of its metabolites to critical proteins. However, knowledge about their molecular reaction mechanisms is scarce. Herein, we have provided density functional theory (DFT) simulation evidences for the reaction mechanisms of the nitroso metabolite of TNT with the sulfhydryl group of model thiols for the first time. The results show that the solvent-mediated proton-transfer mechanism plays a significant role in the entire process. For the formation of semimercaptal, the mechanism is slightly different from the previous one where the thiolate anion attacks the nitroso group. The rearrangement of semimercaptal needs to be triggered by an acid or hydrated ion (H₃O⁺), which is consistent with the previous assumption. The other pathway, the conversion of semimercaptal to hydroxylamine, has to overcome a higher barrier, although it does not need the participation of an acid or a hydrated ion. In addition, the details on transition states, intermediates and free energy surfaces for three reactions are given, which make up for the lack of experimental knowledge. These conclusions can help to deeply understand the toxic effects of TNT and other nitroaromatic explosives.

The critical role of porcine cytochrome P450 3A46 in the bioactivation of aflatoxin B1

Aflatoxin B₁ (AFB₁) is bioactivated by cytochrome P450 (CYP) 3A isoforms in humans to generate the highly reactive epoxide intermediate AFB₁-8,9-epoxide (AFBO), causing hepatotoxicity and hepatocarcinoma. Due to the unavoidable contamination in their feed, pigs are more likely to be exposed to AFB₁ and indirectly harm human health. Therefore, identifying the porcine CYP3A isoforms involved in AFB₁-8,9-epoxidation is critical. In this study, we used codon optimization and N-terminal coding sequence modification to modify a CYP3A46 recombinant protein that exhibits good structure and catalytic activities and revealed its strong AFB₁-8,9-epoxidase activity for the first time. Site-directed mutagenesis, kinetics and docking analyses were performed and demonstrated that residues Phe-108, Ser-119, Phe-215, Phe-304 and Thr-309 play important roles in AFB₁-8,9-epoxidation and its responsiveness to α-naphthoflavone. Interestingly, we uncovered the dual and reverse roles of Phe-304 in CYP3A46, CYP3A5 and CYP3A4 in AFB₁ oxidation. Unlike the π-π interaction between the Phe-304 phenyl of CYP3A4 and the AFB₁ aromatic ring, Phe-304 of CYP3A46 may function to provide steric hindrance to bind AFB₁. Phe-108 and Phe-215 could stabilize AFB₁ with a potentially productive orientation through van der Waals interactions with AFB₁. Ser-119 and Thr-309 are likely to function to form H-bonds with AFB₁. This study broadens our knowledge of AFB₁ bioactivation in pigs and may contribute to reduce the deleterious effects of AFB₁ in pigs and humans.

Interaction Effects of AFB1 and MC-LR Co-exposure with Polymorphism of Metabolic Genes on Liver Damage: focusing on SLCO1B1 and GSTP1

AFB1 and MC-LR are two major environmental risk factors for liver damage worldwide, especially in warm and humid areas, but there are individual differences in health response of the toxin-exposed populations. Therefore, we intended to identify the susceptible genes in transport and metabolic process of AFB1 and MC-LR and find their effects on liver damage. We selected eight related SNPs that may affect liver damage outcomes in AFB1 and MC-LR exposed persons, and enrolled 475 cases with liver damage and 475 controls of healthy people in rural areas of China. The eight SNPs were genotyped by PCR and restriction fragment length polymorphism. We found that SLCO1B1 (T521C) is a risk factor for liver damage among people exposed to high AFB1 levels alone or combined with MC-LR, and that GSTP1 (A1578G) could indicate the risk of liver damage among those exposed to high MC-LR levels alone or combined with high AFB1 levels. However, GSTP1 (A1578G) could reduce the risk of liver damage in populations exposed to low MC-LR levels alone or combined with high AFB1 levels. In conclusion, SLCO1B1 (T521C) and GSTP1 (A1578G) are susceptible genes for liver damage in humans exposed to AFB1 and/or MC-LR in rural areas of China.

Molecular dynamics investigation of stereoselective inhibition mechanism of HIF-2α/ARNT heterodimer

Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors related with the onset and progression of solid tumors. Studies demonstrated a class of tetrazole containing chiral inhibitors could stereoselectively disrupt the HIF-2 dimerization and reduce the target gene expression. However, the dynamical features and structural motifs of the HIF-2 heterodimer caused by the binding of enantiomers have not been rationalized at the atomistic level. In this work, molecular dynamics (MD) simulations combined with adaptive steered MD (ASMD) simulations were used to investigate stereoselective interrupting mechanism of HIF-2. Our results decipher that the binding of ligand A (S, R)-24 begets the significant conformation changes of β-sheets and interrupts the HIF-2α/ARNT heterodimerization, which may be attributed to the disruption of the hydrogen bond and salt bridge interactions formed by the 4 foremost residues (Asp240, Arg247, Glu362, and Arg366) and the destruction of hydrophobic interactions on the binding interface. By contrast, the binding of ligand B (R, S)-24 does not disrupt protein dimerization and causes the motion of Fα helix in HIF-2α PAS-B domain to further change the major tunnel for ligand ingress and engress. The present work provides important molecular-level insight into the effect of the binding enantiomers on HIF-2 heterodimerization and bridges the gap between theory and the experimental results, which may conduce to develop highly potent antagonists for intervening the HIF-2-driven tumors.

Interactions of omeprazole-based analogues with cytochrome P450 2C19: a computational study

Cytochrome P450 2C19 (CYP2C19) is one of 57 drug metabolizing enzymes in humans and is responsible for the metabolism of ∼7-10% of drugs in clinical use. Recently omeprazole-based analogues were reported to be the potent inhibitors of CYP2C19 and have the potential to be used as the tool compounds for studying the substrate selectivity of CYP2C19. However, the binding modes of these compounds with CYP2C19 remain to be elucidated. In this study, a combination of molecular docking, molecular dynamics (MD), and MM/GBSA calculations was employed to systematically investigate the interactions between these compounds and CYP2C19. The binding modes of these analogues were analyzed in detail. The results indicated that the inclusion of explicit active site water molecules could improve binding energy prediction when the water molecules formed a hydrogen bonding network between the ligand and protein. We also found that the effect of active site water molecules on binding free energy prediction was dependent on the ligand binding modes. Our results unravel the interactions of these omeprazole-based analogues with CYP2C19 and might be helpful for the future design of potent CYP2C19 inhibitors with improved metabolic properties.

Dissecting the Cytochrome P450 1A2- and 3A4-Mediated Metabolism of Aflatoxin B1 in Ligand and Protein Contributions

Aflatoxin B1 (AFB1) is a chemically intriguing compound because it has several potential sites of metabolism (SOMs), although only some of them are observed experimentally. Cytochrome P450 (CYP) 3A4 and 1A2 are the major isoforms involved in its metabolism. Here, we systematically investigate reactivity and accessibility of all possible SOMs in these two CYPs to elucidate AFB1 metabolism. DFT calculations were used to determine activation energies for each possible reaction. Aliphatic hydroxylation on position 9A and 3α are energetically favored, whereas position 9 is the preferred site for epoxidation. Docking studies, molecular dynamics (MD) simulations, and free energy (MM/GBSA) calculations were applied to elucidate the accessibility of each SOM. The most stable binding modes in CYP3A4 favor the formation of the 3α-hydroxylated and 8,9-exo-epoxide metabolites. Conversion of the methoxy group is also sterically possible, but not observed experimentally due to its low reactivity. In the CYP1A2 active site, AFB1 cannot orient position 3 towards the catalytic center, whereas the 8,9-exo-epoxide and 9A-hydroxylated metabolites are formed from the most stable and the 8,9-endo-epoxide from a less stable binding mode, respectively. The results agree with experimental data and suggest that both reactivity and the shape of the enzyme active site need to be considered to understand the distribution of SOMs and to improve current SOM prediction methods.

Procarcinogens - Determination and Evaluation by Yeast-Based Biosensor Transformed with Plasmids Incorporating RAD54 Reporter Construct and Cytochrome P450 Genes

In Vietnam, a great number of toxic substances, including carcinogens and procarcinogens, from industrial and agricultural activities, food production, and healthcare services are daily released into the environment. In the present study, we report the development of novel yeast-based biosensor systems to determine both genotoxic carcinogens and procarcinogens by cotransformation with two plasmids. One plasmid is carrying human CPR and CYP (CYP3A4, CYP2B6, or CYP2D6) genes, while the other contains the RAD54-GFP reporter construct. The three resulting coexpression systems bearing both CPR-CYP and RAD54-GFP expression cassettes were designated as CYP3A4/CYP2B6/CYP2D6 + RAD54 systems, respectively and used to detect and evaluate the genotoxic potential of carcinogens and procarcinogens by selective activation and induction of both CPR-CYP and RAD54-GFP expression cassettes in response to DNA damage. Procarcinogens were shown to be predominantly, moderately or not bioactivated by one of the CYP enzymes and thus selectively detected by the specific coexpression system. Aflatoxin B₁ and benzo(a)pyrene were predominantly detected by the CYP3A4 + RAD54 system, while N-nitrosodimethylamine only moderately activated the CYP2B6 + RAD54 reporter system and none of them was identified by the CYP2D6 + RAD54 system. In contrast, the genotoxic carcinogen, methyl methanesulfonate, was detected by all systems.

Our yeast-reporter system can be performed in 384-well microplates to provide efficient genotoxicity testing to identify various carcinogenic compounds and reduce chemical consumption to about 53% as compared with existing 96-well genotoxicity bioassays. In association with a liquid handling robot, this platform enables rapid, cost-effective, and high-throughput screening of numerous analytes in a fully automated and continuous manner without the need for user interaction.

Elucidating a chemical defense mechanism of Antarctic sponges: A computational study

In 2000, a novel secondary metabolite (erebusinone, Ereb) was isolated from the Antarctic sea sponge, Isodictya erinacea. The bioactivity of Ereb was investigated, and it was found to inhibit molting when fed to the arthropod species Orchomene plebs. Xanthurenic acid (XA) is a known endogenous molt regulator present in arthropods. Experimental studies have confirmed that XA inhibits molting by binding to either (or both) of two P450 enzymes (CYP315a1 or CYP314a1) that are responsible for the final two hydroxylations in the production of the molt-inducing hormone, 20-hydroxyecdysone (20E). The lack of crystal structures and biochemical assays for CYP315a1 or CYP314a1, has prevented further experimental exploration of XA and Ereb's molt inhibition mechanisms. Herein, a wide array of computational techniques - homology modeling, molecular dynamics simulations, binding site bioinformatics, flexible receptor-flexible ligand docking, and molecular mechanics-generalized Born surface area calculations - have been employed to elucidate the structure-function relationships between the aforementioned P450s and the two described small molecule inhibitors (Ereb and XA). Results indicate that Ereb likely targets CYP315a1 by interacting with a network of aromatic residues in the binding site, while XA may inhibit both CYP315a1 and CYP314a1 because of its aromatic, as well as charged nature.

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

Cyclodextrins (CDs) have been extensively utilized as host molecules to enhance the solubility, stability and bioavailability of hydrophobic drug molecules through the formation of inclusion complexes. It was previously reported that the use of co-solvents in such studies may result in ternary (host:guest:co-solvent) complex formation. The objective of this work was to investigate the effect of ethanol as a co-solvent on the inclusion complex formation between α-mangostin (α-MGS) and β-CD, using both experimental and theoretical studies. Experimental phase-solubility studies were carried out in order to assess complex formation, with the mechanism of association being probed using a mathematical model. It was found that α-MGS was poorly soluble at low ethanol concentrations (0–10% v/v), but higher concentrations (10–40% v/v) resulted in better α-MGS solubility at all β-CD concentrations studied (0–10 mM). From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1), even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co-solvent enhances the solubility of α-MGS with some effects on the binding affinity with β-CD, depending on the concentration employed.

Pi-pi Stacking Mediated Cooperative Mechanism for Human Cytochrome P450 3A4

Human Cytochrome P450 3A4 (CYP3A4) is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate metabolism efficiency. In the current study, we constructed both normal and cooperative binding models of human CYP3A4 with antifungal drug ketoconazoles (KLN). Molecular dynamics simulation and free energy calculation were then carried out to study the cooperative binding mechanism. Our simulation showed that the second KLN in the cooperative binding model had a positive impact on the first one binding in the active site by two significant pi-pi stacking interactions. The first one was formed by Phe215, functioning to position the first KLN in a favorable orientation in the active site for further metabolism reactions. The second one was contributed by Phe304. This pi-pi stacking was enhanced in the cooperative binding model by the parallel conformation between the aromatic rings in Phe304 and the dioxolan moiety of the first KLN. These findings can provide an atomic insight into the cooperative binding in CYP3A4, revealing a novel pi-pi stacking mechanism for drug-drug interactions.